SMED30033047

Overview
NameSMED30033047
Smed IDSMED30033047
Length (bp)1376
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30033047 (SMED30033047) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033047 (SMED30033047) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30033047 (SMED30033047) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033047 (SMED30033047) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30033047

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30033047SMESG000046962.1 SMESG000046951.1 SMESG000040592.1 SMESG000034034.1 dd_Smed_v4_489_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30033047SMESG000046962.1 SMESG000046951.1 SMESG000040592.1 SMESG000034034.1 dd_Smed_v4_489_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30033047SMESG000046962.1 SMESG000046951.1 SMESG000040592.1 SMESG000034034.1 dd_Smed_v4_489_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30033047SMESG000046962.1 SMESG000046951.1 SMESG000040592.1 SMESG000034034.1 dd_Smed_v4_489_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033047 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002272:9141..10668 -4889
Homology
[Close]
BLAST of SMED30033047 vs. Planmine SMEST
Match: SMESG000034034.1 (SMESG000034034.1)

HSP 1 Score: 546.584 bits (1407), Expect = 0.000e+0
Identity = 288/296 (97.30%), Postives = 290/296 (97.97%), Query Frame = 2 
Query:   89 MFRRTSHCVCPPNSSIKINPINSDHFFQVNNLKNDFLMHSPPLPPRTIKNNFPTKYPSNKNAISEWNDKVNTYDKRVQCSCVRPHSCPAEESSFILTPPIPPKTCTAANSQTKSKNIKTNINDEQSKKVEISQNDNRKSSRYRGIEKTXXXXXXXXXXXXXXXXXXXKLLHTDKLPFTQDNVDIHVNKYFMKNTDNIMEQNCQKSHHKPNELCKICDSNAIKFQRRPFVDMINPPLNHAPDLIVDRSNSMGIGAQSTQPQKSNKFRNKLKSKLTQLWSKSKKSVDNSPIKIDPTLA 976
            MFRRTSHCVCPPNSSIKINPINSDHFFQVN LKNDFLMHSPPLPPRTIKNNFPTKYPSNKNAISEWNDKVNTYDKRVQCSCVRPHSCPAEESSFILTPPIPPKTCTAANSQTKSKNIKTNINDEQSKKVEISQNDNRKSSRYRGIEKTNSRKKSRSNSRSVVRDDKSKLLHTDKLPFTQDNVDIHVNKYFMKNTDN+MEQNCQKSHHKPNELCKICDSNAIKFQRRPFVDMINPPLNHAPDLIVDRSNSMGIGAQSTQPQKSNKFRNKLKSKLTQLWSKSKKSVDNSPI  D  + 
Sbjct:    1 MFRRTSHCVCPPNSSIKINPINSDHFFQVNTLKNDFLMHSPPLPPRTIKNNFPTKYPSNKNAISEWNDKVNTYDKRVQCSCVRPHSCPAEESSFILTPPIPPKTCTAANSQTKSKNIKTNINDEQSKKVEISQNDNRKSSRYRGIEKTNSRKKSRSNSRSVVRDDKSKLLHTDKLPFTQDNVDIHVNKYFMKNTDNLMEQNCQKSHHKPNELCKICDSNAIKFQRRPFVDMINPPLNHAPDLIVDRSNSMGIGAQSTQPQKSNKFRNKLKSKLTQLWSKSKKSVDNSPINRDTVIT 296

HSP 2 Score: 199.134 bits (505), Expect = 2.632e-55
Identity = 116/119 (97.48%), Postives = 117/119 (98.32%), Query Frame = 3 
Query:  951 QSKLTQLWPKSKKSVDNSPINRDTVITPENSHALKYPDDTTPRPRRSKSLHLIPDSSLSPKTSMQTKSSVHTSTDASITKNSSIFAVISPSTARWKRNLFCIXXXXXXXXXXXXXXFDC 1307
            +SKLTQLW KSKKSVDNSPINRDTVITPENSHALKYPDDTT RPRRSKSLHLIPDSSLSPKTSMQTKSSVHTSTDASITKNSSIFAVISPSTARWKRNLFCISPKAGGSGSSNSKKFDC
Sbjct:  270 KSKLTQLWSKSKKSVDNSPINRDTVITPENSHALKYPDDTTLRPRRSKSLHLIPDSSLSPKTSMQTKSSVHTSTDASITKNSSIFAVISPSTARWKRNLFCISPKAGGSGSSNSKKFDC 388
[Close]
BLAST of SMED30033047 vs. Planmine SMEST
Match: SMESG000034034.1 (SMESG000034034.1)

HSP 1 Score: 471.085 bits (1211), Expect = 6.986e-156
Identity = 252/259 (97.30%), Postives = 254/259 (98.07%), Query Frame = 2 
Query:  200 MHSPPLPPRTIKNNFPTKYPSNKNAISEWNDKVNTYDKRVQCSCVRPHSCPAEESSFILTPPIPPKTCTAANSQTKSKNIKTNINDEQSKKVEISQNDNRKSSRYRGIEKTXXXXXXXXXXXXXXXXXXXKLLHTDKLPFTQDNVDIHVNKYFMKNTDNIMEQNCQKSHHKPNELCKICDSNAIKFQRRPFVDMINPPLNHAPDLIVDRSNSMGIGAQSTQPQKSNKFRNKLKSKLTQLWSKSKKSVDNSPIKIDPTLA 976
            MHSPPLPPRTIKNNFPTKYPSNKNAISEWNDKVNTYDKRVQCSCVRPHSCPAEESSFILTPPIPPKTCTAANSQTKSKNIKTNINDEQSKKVEISQNDNRKSSRYRGIEKTNSRKKSRSNSRSVVRDDKSKLLHTDKLPFTQDNVDIHVNKYFMKNTDN+MEQNCQKSHHKPNELCKICDSNAIKFQRRPFVDMINPPLNHAPDLIVDRSNSMGIGAQSTQPQKSNKFRNKLKSKLTQLWSKSKKSVDNSPI  D  + 
Sbjct:    1 MHSPPLPPRTIKNNFPTKYPSNKNAISEWNDKVNTYDKRVQCSCVRPHSCPAEESSFILTPPIPPKTCTAANSQTKSKNIKTNINDEQSKKVEISQNDNRKSSRYRGIEKTNSRKKSRSNSRSVVRDDKSKLLHTDKLPFTQDNVDIHVNKYFMKNTDNLMEQNCQKSHHKPNELCKICDSNAIKFQRRPFVDMINPPLNHAPDLIVDRSNSMGIGAQSTQPQKSNKFRNKLKSKLTQLWSKSKKSVDNSPINRDTVIT 259

HSP 2 Score: 199.134 bits (505), Expect = 2.362e-55
Identity = 116/119 (97.48%), Postives = 117/119 (98.32%), Query Frame = 3 
Query:  951 QSKLTQLWPKSKKSVDNSPINRDTVITPENSHALKYPDDTTPRPRRSKSLHLIPDSSLSPKTSMQTKSSVHTSTDASITKNSSIFAVISPSTARWKRNLFCIXXXXXXXXXXXXXXFDC 1307
            +SKLTQLW KSKKSVDNSPINRDTVITPENSHALKYPDDTT RPRRSKSLHLIPDSSLSPKTSMQTKSSVHTSTDASITKNSSIFAVISPSTARWKRNLFCISPKAGGSGSSNSKKFDC
Sbjct:  233 KSKLTQLWSKSKKSVDNSPINRDTVITPENSHALKYPDDTTLRPRRSKSLHLIPDSSLSPKTSMQTKSSVHTSTDASITKNSSIFAVISPSTARWKRNLFCISPKAGGSGSSNSKKFDC 351
The following BLAST results are available for this feature:
BLAST of SMED30033047 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30033047 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000034034.12.632e-5597.30SMESG000034034.1[more]
SMESG000034034.16.986e-15697.30SMESG000034034.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033047 ID=SMED30033047|Name=SMED30033047|organism=Schmidtea mediterranea sexual|type=transcript|length=1376bp
CAAAAACATTTTTAAAACAAAATTTAATGTTTTACTTTGTTTATTATTAT
AATTGAAACTATAGGAATATTTAGAAGATAGTTATGCAATGTTCAGAAGA
ACATCGCACTGTGTGTGCCCGCCCAATTCCTCCATTAAAATTAATCCTAT
AAATTCTGATCATTTCTTCCAAGTAAATAATTTAAAAAATGATTTCCTGA
TGCACTCACCACCTCTACCACCAAGAACTATTAAAAATAACTTTCCAACA
AAATATCCTTCGAATAAGAATGCCATTTCTGAGTGGAATGATAAGGTTAA
TACTTATGATAAACGGGTTCAATGTAGCTGTGTTAGACCTCATTCATGTC
CAGCTGAAGAATCTTCATTTATTTTAACACCTCCAATTCCACCAAAAACT
TGTACAGCAGCTAATTCTCAAACGAAATCTAAAAATATCAAAACCAATAT
AAACGACGAACAATCAAAAAAAGTGGAAATATCTCAAAATGATAATCGAA
AATCAAGTCGGTACAGAGGAATAGAAAAAACTAATAGTCGTAAAAAGTCT
CGTAGTAACTCAAGATCAGTCGTGAGAGATGATAAATCTAAACTATTGCA
CACGGATAAATTACCTTTCACACAAGACAATGTCGACATCCACGTGAATA
AATATTTCATGAAAAACACCGATAATATCATGGAACAGAACTGCCAAAAA
TCCCATCATAAACCTAATGAATTGTGTAAAATCTGTGACAGCAACGCAAT
AAAATTCCAAAGGCGACCATTTGTCGACATGATCAATCCTCCGTTAAATC
ATGCGCCAGATCTTATTGTCGATCGATCAAACTCGATGGGGATTGGCGCG
CAATCGACACAACCACAAAAATCCAACAAATTCCGCAACAAATTGAAATC
AAAATTGACCCAACTCTGGTCAAAATCGAAAAAATCAGTCGACAATTCGC
CAATCAAAATTGACCCAACTCTGGCCAAAATCGAAAAAATCAGTCGACAA
TTCGCCAATCAATCGAGACACTGTGATAACTCCGGAAAATTCTCACGCTC
TCAAATACCCCGACGACACAACACCGCGTCCTCGACGATCGAAAAGTCTT
CATTTAATTCCCGATAGCAGTCTTTCACCGAAAACCTCTATGCAAACGAA
ATCATCTGTTCACACATCGACAGATGCGAGCATCACGAAAAATTCCAGCA
TTTTCGCCGTCATATCGCCGAGCACAGCGAGATGGAAGCGAAATCTATTT
TGCATTTCACCGAAAGCCGGTGGCAGCGGCTCATCCAATAGCAAGAAATT
CGACTGTGCAATGTCCATGGGTAACGCGACAAACAATACCAACAGTAACG
GCAATAACGGCAACAACAACGGCAAC
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protein sequence of SMED30033047-orf-1

>SMED30033047-orf-1 ID=SMED30033047-orf-1|Name=SMED30033047-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=343bp
MFRRTSHCVCPPNSSIKINPINSDHFFQVNNLKNDFLMHSPPLPPRTIKN
NFPTKYPSNKNAISEWNDKVNTYDKRVQCSCVRPHSCPAEESSFILTPPI
PPKTCTAANSQTKSKNIKTNINDEQSKKVEISQNDNRKSSRYRGIEKTNS
RKKSRSNSRSVVRDDKSKLLHTDKLPFTQDNVDIHVNKYFMKNTDNIMEQ
NCQKSHHKPNELCKICDSNAIKFQRRPFVDMINPPLNHAPDLIVDRSNSM
GIGAQSTQPQKSNKFRNKLKSKLTQLWSKSKKSVDNSPIKIDPTLAKIEK
ISRQFANQSRHCDNSGKFSRSQIPRRHNTASSTIEKSSFNSR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000099neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 277..297
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 120..167
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 277..300
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 106..167